Safaa Fathy was as surprised to discover that she is at the heart of a plot against America as she was to hear that her small Tennessee town is a focus of hate in the Muslim world.

The diminutive fifty-something physiotherapist, who has lived in Murfreesboro for most of her adult life, happens to be on the board of her town's Islamic centre. Now she finds herself accused of being a front for Islamic Jihad, of planning to impose sharia law on her neighbours, and of threatening the very existence of Christianity in Tennessee.

"There is something around the whole United States, something is different. I was here since 1982. I have three kids here and I never had any trouble. My kids, they go to the girl scouts, they play basketball, they did all the normal activities. It just started this year. It's strange, because after 9/11 there was no problem," said Fathy, who was born in Egypt. "In the past in America other people were the target. We are the target now. We have trouble in California, we have trouble in New York, we have trouble in Florida. It's a shame because Murfreesboro is a very nice town to live in."

As the US prepares to mark the ninth anniversary of the al-Qaida assault on New York and the Pentagon, the country's Muslims say they are enduring a wave of hostility and suspicion from some of their fellow Americans that they rarely encountered in the years immediately following the 9/11 attacks.

The increasingly bitter dispute over plans to build an Islamic centre and mosque two blocks from Ground Zero in New York is part of it, fuelling a debate about whether Muslims in the US put their faith before their country. Opponents of the mosque plan to mark the anniversary with a rally in New York today led by a leading anti-Islamic activist, Pamela Geller, who has the support of prominent Republican politicians given to increasingly strident anti-Muslim rhetoric. Among those expected to speak is Geert Wilders, the virulently anti-Islamic Dutch political leader.

Even the possibly rescinded threat by a publicity-seeking pastor in Florida to burn hundreds of copies of the Qur'an played into the hands of Islam's foes in America, despite the fact it did not garner much popular support, when it drew threats of bloody retribution from some Muslim groups abroad. All this comes against a backdrop of growing numbers of Americans suspecting that their president is secretly a Muslim – nearly one in five say that he is and many more think it likely – and diminishing support for the wars in Afghanistan and Iraq, which are still proving a heavy burden in blood and money. The charged atmosphere in which the terrorist attacks will be remembered this weekend has also penetrated deep into the heartland, where hostility has increasingly shifted inward to focus on America's own Islamic communities. "It really started in May," said Fathay. "I keep asking myself, why this year? Why are they suddenly lying about us now?"

Late last year Musfreesboro's Islamic leaders announced plans to build a new mosque because the 250 Muslim families in town had outgrown the existing one. The construction plans were approved. At first, no one in the town of about 100,000 people south of Nashville said much about it.

In February someone spray-painted over the sign: "Not welcome", with the letter t shaped like a Christian cross. Fathay put that down to one hostile individual. But by May protest meetings were organised, politicians were denouncing the plans and the loyalty of Muslims in the town was openly questioned. Critics did not pull their punches at a public meeting. Among those who spoke against construction of the new Islamic centre was Karen Harrell.

"Everybody knows they are trying to kill us. People are really concerned about this. Somebody has to stand up and take this country back," she said.

Speakers accused Muslims in the town of promoting polygamy and indoctrinating the young with hate, and questioned whether they adhered to the US constitution.

George Erdel, running for a seat in the US Congress as a "Tea Party Democrat", feared that the true intent of the mosque was to impose Islamic rule. "Islam is a system of government. Islam is a system of justice. We've got people here who remember September 11 2001. These people are scared," he said. "I'm afraid we'll have a training facility."

It did not go unnoticed by Islamic leaders that some of the fiercest criticism was whipped up by candidates in this year's elections. At the forefront was Lou Ann Zelenik, a candidate for the Republican nomination for Congress who is a leader of the local Tea Party movement.

"This 'Islamic Centre' is not part of a religious movement; it is a political movement designed to fracture the moral and political foundation of Middle Tennessee," Zelenik said. "Until the American Muslim community find it in their hearts to separate themselves from their evil, radical counterparts, to condemn those who want to destroy our civilisation and will fight against them, we are not obligated to open our society to any of them."

Alongside Zelenik was Laurie Cardoza-Moore, the founder of a group that rallies Christians in support of Israel. Cardoza-Moore describes herself as "a leader who successfully stewards masses toward her intended outcomes".

She told a Christian television station that the plan to build a new mosque in Murfreesboro was part of a plot to take over Middle Tennessee because it is the heart of the Bible belt:

"You have Bible book publishers. You have Christian book publishers. You have Christian music headquartered here. The radical Islamic extremists have stated that they are still fighting the Crusaders, and they see this as the capital of the Crusaders."

Similar warnings can be heard in other parts of Tennessee and in states from California to New England.

The imam of the Murfreesboro mosque, Ossama Bahloul, says others have been here before. A generation ago in Tennessee black activists were burned out of their homes for agitating against segregation and for civil rights, and Catholics and other Christian minorities were targets for the Ku Klux Klan.

"It's a cycle of life. If we are really dangerous, let them close this [existing] centre too. This community did not do a single act of violence," said Bahloul. "Maybe it has a relationship with the election, maybe with the economic problems we have in the country, maybe it was September 11, but I doubt this, because why did we have a fine time last year and the year before and before that when the memory of September 11 was still fresh in everybody's mind?"

Ron Messier, a professor of Islamic studies who lives in Murfreesboro, says the mood is driven by politics. "It's happened because this is an election year and I think there were some political candidates who thought that here in Middle Tennessee a lot of people have very right leanings and they could gain some political leverage by promoting fear about people who have been here for 20 years or more without ever being an issue," he said. Yet the politicians apparently did not have to drill deep to tap into fears of Muslims, who are subject to language that would not be acceptable when talking about almost any other minority. They are helped by parts of the media. Fox News leads the charge, routinely giving a platform to those who question the loyalty of Muslim Americans and to conspiracy theorists.

This week Martin Peretz, editor-in-chief of New Republic, an influential Washington political magazine, wrote that Muslims were unfit for the protections of the US constitution. "Muslim life is cheap, most notably to Muslims. And among those Muslims led by the Imam Rauf [of the proposed New York Islamic centre] there is hardly one who has raised a fuss about the routine and random bloodshed that defines their brotherhood," Peretz wrote. "So, yes, I wonder whether I need honour these people and pretend that they are worthy of the privileges of the First Amendment which I have in my gut the sense that they will abuse."

Peretz was swiftly denounced by some prominent American bloggers, among them Glenn Greenwald, who writes for Salon.com. "Bigotry against Muslims and Arabs is one of the last acceptable forms of overt bigotry that is tolerated in American political culture. If you look at the things that he said and replace the word Muslim or Arab with Jew or even Christian, those comments would be completely career ending and reputation destroying," he said.

Two weeks ago someone set fire to construction equipment at the site of Murfreesboro's new mosque. Some in the town were outraged, but not Kimberly Kelly. "I think it was a piece of their own medicine. They bombed our country," she told The Tennessean newspaper. Two days later about 150 people turned out for a candlelight vigil in support of the Muslim community on the steps of the local courthouse.

Many in the town say they have no problem with the new mosque. Among them is a woman called Bonnie who works in a local bookshop and lost a stepbrother in one of the World Trade Centre towers.

"I don't have a problem with them opening a mosque in New York, just not two blocks from where my stepbrother died. But here doesn't bother me because everybody has a right to practise their religion. They've been here, they're quiet. They haven't bothered anybody," she said.

Muslim leaders are careful to say that the hostility has come from a vocal minority and has prompted an outpouring of backing from non-Muslims. The Islamic centre has a "wall of support" with messages from people who say they are Christian and have sons fighting in Afghanistan.

The burning question for many Muslims in Murfreesboro is whether, once the political calendar moves on, they will again be left in peace or whether relations have been poisoned for years to come. Perhaps they can draw comfort from August's primary election for Congress. Zelenick was defeated, along with most of the other politicians who made Islam an election issue in Tennessee.